Boron-containing oligodeoxyribonucleotide 14mer duplexes: enzymatic synthesis and melting studies

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Abstract
A set of three 14mer oligodeoxyribonucleotides of sequence d(5′- CTATGGCCTCAG*CT-3′/3′-GATACCGGAGTCGA- 5′) containing G* variants either as 2′-deoxyguanosine phosphate (unmodified), N7-cyanoborane 2′-deoxyguanosine phosphate (base-modified) or 2′-deoxyguanosine boranophosphate (backbonemodified) were synthesized by template-directed primer extension. Both the /V7-cyanoborane ′-deoxyguanosine triphosphate and 2′-deoxyguanosine a-boranotriphosphate nucleotldes are good substrates for Sequenase. We infer that a single Sp boranophosphate linkage (which has a stereochemistry equivalent to the corresponding Rp thiophosphate analog) is formed in the backbone-modified 14mer. Thermally induced helix-coil transitions were monitored for the hybridized duplexes using UV and circular dichroism (CD) spectroscopy. The CD spectra of the two types of boron-modified hybrids closely resemble the unmodified parent duplex, forming B-type helices in 150 mM NaCI, 1 mM EDTA, 10 mM phosphate, pH 7.4, buffer. UV melting results indicate that both hybrids have stabilities comparable with the parent duplex as measured by Tp or δG°25. These studies indicate that singly modified base- or backbone-boronated DNA are good analogs of normal DNA.